Gee said Varley told her he had been putting the baby down and dropped him by accident, causing the injury to his arm.
But after Preston’s death, Gee said Varley gave a different explanation for the injury.
She said: “The inconsistency was around the cot. The first instance was he dropped him, the second was he had his arm out of the cot and hurt it.
“So, no consistency.”
On 27 July 2023 the baby was rushed to hospital by the defendants, unconscious and in a state of cardiac arrest, and medics could not revive him.
Afterwards, Varley told Gee he had put the baby in the bath while he had a shower then realised he did not have a towel, the court heard.
“So he went out and when he came back in the baby had fallen out of the bath seat and was face down in the water,” Gee said.
“When I made the phone call Jamie said to me, ‘Jan, I promise you, I didn’t do anything.
“It was as soon as I made contact, he said, ‘Jan, I promise you, I didn’t do anything’ and went on to give an account of that day.”
But at Blackpool Victoria Infirmary, the child was found to be dry, had dry hair and did not appear to have swallowed any water, the court heard.
A Home Office post-mortem examination found 40 non-accidental, internal and external injuries.
There were bruises and grazes to his head, face and mouth, upper limbs, chest, back and left thigh.
Preston also had injuries to his mouth, throat and bottom.
There was no evidence to support drowning, the court heard.
A pathologist gave the cause of death as acute upper airways obstruction by either smothering or an object or objects inserted into his mouth.
Varley denies murder, manslaughter, two counts of assault by penetration, five counts of cruelty to a child, grievous bodily harm, sexual assault of a child, 13 counts of taking indecent photos or videos of a child, one of distributing an indecent photo of a child, to his co-accused, and one of making an indecent photo.
McGowan-Fazakerley denies allowing the death of a child, three counts of child cruelty and one count of the sexual assault of a child.
The trial continues.